Ligand profile

302

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_00801 — Uracil-DNA glycosylase

Via homolog PDB 2hxm UniProt P13051 Formula C₁₅H₁₄N₄O₆
Mol. weight 346.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
302
PDB
2hxm
UniProt (similar protein)
P13051
Target protein
KP13_00801

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 346.30 Da
LogP (Crippen) 0.16
H-bond donors 3
H-bond acceptors 7
TPSA 146.20 Ų
Rotatable bonds 8
Aromatic rings 2 / 2
Heavy atoms 25
Fraction sp³ C 0.13
Formula C₁₅H₁₄N₄O₆

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 146.2
  • −1 ≤ LogP ≤ 5 0.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 346.3
  • LogP ≤ 5 0.16
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 146.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1\C=N\OCCO/N=C/C2=CC(=O)NC(=O)N2)C(=O)O
InChI 
InChI=1S/C15H14N4O6/c20-13-7-12(18-15(23)19-13)9-17-25-6-5-24-16-8-10-1-3-11(4-2-10)14(21)22/h1-4,7-9H,5-6H2,(H,21,22)(H2,18,19,20,23)/b16-8+,17-9+
InChIKey 
XHDKIDMFBWLHAX-GONBZBRSSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF03167

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_00801.

PDB 15

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)